Reading WGBS data into analysis-ready structures
July 25, 2024
Converting an epigenetic difference into a genetic difference
mC \(\xrightarrow{bisulfite}\) C
C \(\xrightarrow{bisulfite}\) U
Morrison et al. “Dupsifter” (2023, Bioinformatics)
WGBS alignment
Methylation analysis
BSseq: read.bismark \(\to\) bsseq \(\to\) DMRSeq, DMRcate
biscuiteer: readBiscuit \(\to\) BSseq
scMET
Krueger & Andrews “Bismark” (2011, Bioinformatics)
Zhou et al. “BISCUIT” (2024, Nucleic Acids Research)
Hansen et al. “BSmooth” (2012, Genome Biology)
Korthauer et al. “Detection and Accurate False Discovery Rate Control of Differentially Methylated Regions from Whole Genome Bisulfite Sequencing” (2019, Biostatistics)
Peters et al. “Calling Differentially Methylated Regions from Whole Genome Bisulphite Sequencing with DMRcate” (2021, Nucleic Acids Research)
Kapourani et al. “scMET” (2021, Genome Biology)
read.bismark to read Bismark .cov files
M and Coverage count matrices
GRanges storing CpG loci
Used by DMRSeq, DMRcate
An object of type 'BSseq' with
69349 methylation loci
93 samples
has not been smoothed
All assays are in-memory
Hansen et al. “BSmooth” (2012, Genome Biology)
read.bismark to read Bismark .cov files
M and Coverage count matrices
GRanges storing CpG loci
Used by DMRSeq, DMRcate
An object of type 'BSseq' with
69349 methylation loci
93 samples
has not been smoothed
All assays are in-memory
Hansen et al. “BSmooth” (2012, Genome Biology)
htslibCPU: Intel Xeon CPU E5-2698 v4 @ 2.20GHz
CPU: Intel Xeon CPU E5-2698 v4 @ 2.20GHz
CPU: Intel Xeon CPU E5-2698 v4 @ 2.20GHz
CPU: Intel Xeon CPU E5-2698 v4 @ 2.20GHz
iscream is an R package to read WGBS data into analysis-ready data structuresShen lab
Ian Beddows
Svetlana Djirackor
Ben Johnson
Kelly Kryzanowski
Paige Matusiak
Amy Nuffesse (Admin)
Mary Rhodes
Ayush Semwal
Tashi Zandstra
github.com/huishenlab/iscream
James Eapen | Bioconductor 2024 | VAI Department of Epigenetics